PDBsum entry 6seh

DNA binding protein

PDB id: 6seh

Contents

Protein chains

252 a.a.

82 a.a.

77 a.a.

Metals

_ZN ×4

Waters ×10

PDB id:

6seh

Name:

DNA binding protein

Title:

Recognition and processing of branched DNA substrates by slx1-slx4 nuclease

Structure:

Structure-specific endonuclease subunit slx1. Chain: c, a. Engineered: yes. Mutation: yes. Structure-specific endonuclease subunit slx4. Chain: d, b. Engineered: yes

Source:

Thielavia terrestris. Organism_taxid: 35720. Gene: slx1, thite_2107775. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: slx4, tt172_locus87. Expression_system_taxid: 562

Resolution:

3.15Å R-factor: 0.207 R-free: 0.254

Authors:

V.Gaur,W.Zajko,S.Nirwal,A.Szlachcic,M.Gapinska,M.Nowotny

Key ref:

V.Gaur et al. (2019). Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. Nucleic Acids Res, 47, 11681-11690. PubMed id: 31584081 DOI: 10.1093/nar/gkz842

Date:

30-Jul-19 Release date: 25-Sep-19

Protein chains

G2QV68  (G2QV68_THITE) -  GIY-YIG domain-containing protein from Thermothielavioides terrestris (strain ATCC 38088 / NRRL 8126)

Seq: 324 a.a.

Struc: 252 a.a.*

Protein chain

A0A3S4CYR8  (A0A3S4CYR8_9PEZI) -  Structure-specific endonuclease subunit SLX4 from Thermothielavioides terrestris

Seq: 675 a.a.

Struc: 82 a.a.

Protein chain

A0A3S4CYR8  (A0A3S4CYR8_9PEZI) -  Structure-specific endonuclease subunit SLX4 from Thermothielavioides terrestris

Seq: 675 a.a.

Struc: 77 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains C, A: E.C.3.1.-.-

DOI no: 10.1093/nar/gkz842

Nucleic Acids Res 47:11681-11690 (2019)

PubMed id: 31584081

Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease.

V.Gaur, W.Ziajko, S.Nirwal, A.Szlachcic, M.Gapińska, M.Nowotny.

ABSTRACT

Structure-selective endonucleases cleave branched DNA substrates. Slx1 is unique among structure-selective nucleases because it can cleave all branched DNA structures at multiple sites near the branch point. The mechanism behind this broad range of activity is unknown. The present study structurally and biochemically investigated fungal Slx1 to define a new protein interface that binds the non-cleaved arm of branched DNAs. The DNA arm bound at this new site was positioned at a sharp angle relative to the arm that was modeled to interact with the active site, implying that Slx1 uses DNA bending to localize the branch point as a flexible discontinuity in DNA. DNA binding at the new interface promoted a disorder-order transition in a region of the protein that was located in the vicinity of the active site, potentially participating in its formation. This appears to be a safety mechanism that ensures that DNA cleavage occurs only when the new interface is occupied by the non-cleaved DNA arm. Models of Slx1 that interacted with various branched DNA substrates were prepared. These models explain the way in which Slx1 cuts DNA toward the 3' end away from the branch point and elucidate the unique ability of Slx1 to cleave various DNA structures.